Many methods have been developed to ligate double stranded DNA fragments into larger molecules. Assembly methods that allow the user to dictate the order and orientation of the assembled fragments invariably rely on the specific hybridization of short single-stranded overhangs at the fragment ends. In standard cloning methods, these overhangs are generated by restriction enzymes and are typically only 4 nucleotides long. While 4 nucleotides can provide enough specificity in a simple reaction (e.g., 2-6 fragments), they are not useful for more complicated assemblies. In other methods, the double stranded DNA at fragment ends is converted into single stranded overhangs by an exonuclease. Here the single stranded regions can be hundreds of nucleotides long depending on the processivity of the exonuclease. These long regions of single-stranded DNA can provide very good specificity in an assembly, but the processed ends usually have to be repaired using DNA polymerases that can introduce synthesis errors in the product molecules. Additionally, shorter DNA fragments (e.g., less than ˜500 bp) can be entirely degraded by the exonuclease activity before assembly is complete. A third approach is to convert the entire double stranded fragments into single stranded molecules by melting. Complementary regions of homology ˜15-500 nucleotides long at the ends of these fragments can then act as primer sites for DNA polymerases to convert the annealed molecules into a double stranded product. Again, this approach is prone to synthesis errors as well as assembly errors due to inadvertent hybridization between regions of homology elsewhere in the molecules.